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Showing NP-Card for 2-Octenedioic acid (NP0000968)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:19:45 UTC
NP-MRD IDNP0000968
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Octenedioic acid
Description2-Octenedioic acid is an unsaturated dicarboxylic acid found in the urine of persons with abnormal fatty acid metabolism, such as patients with Dicarboxylic aciduria (PMID 2094705 , 2614263 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000968 (2-Octenedioic acid)


  Mrv1652305261923552D          

 12 11  0  0  0  0            999 V2000
   10.4139  -10.9515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6993  -12.1891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9834  -11.3640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6980  -10.1265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5559  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2704  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8414  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9849  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1269  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6993  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4124  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6980  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  2  0  0  0  0
  3 12  1  0  0  0  0
  4 12  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
M  END
Download

3D MOL for NP0000968 (2-Octenedioic acid)

HMDB0000341
     RDKit          3D
2-Octenedioic acid
 24 23  0  0  0  0  0  0  0  0999 V2000
    3.8022   -0.1529    2.0606 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6905    0.7457    1.1920 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5342    1.8416    1.1537 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6375    0.6212    0.1997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8149   -0.4101    0.2066 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7677   -0.4797   -0.8258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5839   -0.4965   -0.1037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6334   -0.5700   -1.2073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0126   -0.5883   -0.5619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1274    0.6668    0.2102 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4516    1.7215   -0.3822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8676    0.6143    1.5675 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4748    1.8011    0.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5187    1.3830   -0.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8921   -1.1907    0.9405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9040   -1.4287   -1.3792 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7847    0.4012   -1.4966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7414    0.4038    0.4867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6899   -1.4469    0.4702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4966    0.3258   -1.8425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -1.4898   -1.7734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0948   -1.4406    0.1224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7683   -0.6537   -1.3703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9328    1.4380    2.1448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
  9 23  1  0
 12 24  1  0
M  END
Download

3D SDF for NP0000968 (2-Octenedioic acid)


  Mrv1652305261923552D          

 12 11  0  0  0  0            999 V2000
   10.4139  -10.9515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6993  -12.1891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9834  -11.3640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6980  -10.1265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5559  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2704  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8414  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9849  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1269  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6993  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4124  -11.3640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6980  -10.9515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  2  0  0  0  0
  3 12  1  0  0  0  0
  4 12  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000968

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CCCC\C=C\C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H12O4/c9-7(10)5-3-1-2-4-6-8(11)12/h3,5H,1-2,4,6H2,(H,9,10)(H,11,12)/b5-3+

> <INCHI_KEY>
BNTPVRGYUHJFHN-HWKANZROSA-N

> <FORMULA>
C8H12O4

> <MOLECULAR_WEIGHT>
172.1785

> <EXACT_MASS>
172.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.606335881515626

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E)-oct-2-enedioic acid

> <ALOGPS_LOGP>
1.14

> <JCHEM_LOGP>
1.3776151823333334

> <ALOGPS_LOGS>
-1.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.910202421504832

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.145957184965917

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
43.03430000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.06e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(E)-oct-2-enedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000968 (2-Octenedioic acid)

HMDB0000341
     RDKit          3D
2-Octenedioic acid
 24 23  0  0  0  0  0  0  0  0999 V2000
    3.8022   -0.1529    2.0606 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6905    0.7457    1.1920 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5342    1.8416    1.1537 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6375    0.6212    0.1997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8149   -0.4101    0.2066 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7677   -0.4797   -0.8258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5839   -0.4965   -0.1037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6334   -0.5700   -1.2073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0126   -0.5883   -0.5619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1274    0.6668    0.2102 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4516    1.7215   -0.3822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8676    0.6143    1.5675 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4748    1.8011    0.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5187    1.3830   -0.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8921   -1.1907    0.9405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9040   -1.4287   -1.3792 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7847    0.4012   -1.4966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7414    0.4038    0.4867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6899   -1.4469    0.4702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4966    0.3258   -1.8425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -1.4898   -1.7734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0948   -1.4406    0.1224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7683   -0.6537   -1.3703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9328    1.4380    2.1448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
  9 23  1  0
 12 24  1  0
M  END
Download

PDB for NP0000968 (2-Octenedioic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  O   UNK     0      19.439 -20.443   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      18.105 -22.753   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       7.436 -21.213   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       8.770 -18.903   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      14.104 -20.443   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.438 -21.213   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.771 -21.213   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.772 -20.443   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.437 -20.443   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.105 -21.213   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.103 -21.213   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.770 -20.443   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   12                                                            
CONECT    4   12                                                            
CONECT    5    6    7                                                       
CONECT    6    5    8                                                       
CONECT    7    5    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    1    2    8                                                  
CONECT   11    9   12                                                       
CONECT   12    3    4   11                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for NP0000968 (2-Octenedioic acid)

COMPND    HMDB0000341
HETATM    1  O1  UNL     1       3.802  -0.153   2.061  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.690   0.746   1.192  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.534   1.842   1.154  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.638   0.621   0.200  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.815  -0.410   0.207  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.768  -0.480  -0.826  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.584  -0.497  -0.104  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.633  -0.570  -1.207  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.013  -0.588  -0.562  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.127   0.667   0.210  1.00  0.00           C  
HETATM   11  O3  UNL     1      -3.452   1.722  -0.382  1.00  0.00           O  
HETATM   12  O4  UNL     1      -2.868   0.614   1.567  1.00  0.00           O  
HETATM   13  H1  UNL     1       5.475   1.801   0.750  1.00  0.00           H  
HETATM   14  H2  UNL     1       2.519   1.383  -0.562  1.00  0.00           H  
HETATM   15  H3  UNL     1       1.892  -1.191   0.940  1.00  0.00           H  
HETATM   16  H4  UNL     1       0.904  -1.429  -1.379  1.00  0.00           H  
HETATM   17  H5  UNL     1       0.785   0.401  -1.497  1.00  0.00           H  
HETATM   18  H6  UNL     1      -0.741   0.404   0.487  1.00  0.00           H  
HETATM   19  H7  UNL     1      -0.690  -1.447   0.470  1.00  0.00           H  
HETATM   20  H8  UNL     1      -1.497   0.326  -1.843  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.421  -1.490  -1.773  1.00  0.00           H  
HETATM   22  H10 UNL     1      -3.095  -1.441   0.122  1.00  0.00           H  
HETATM   23  H11 UNL     1      -3.768  -0.654  -1.370  1.00  0.00           H  
HETATM   24  H12 UNL     1      -2.933   1.438   2.145  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5    5   14
CONECT    5    6   15
CONECT    6    7   16   17
CONECT    7    8   18   19
CONECT    8    9   20   21
CONECT    9   10   22   23
CONECT   10   11   11   12
CONECT   12   24
END
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SMILES for NP0000968 (2-Octenedioic acid)

OC(=O)CCCC\C=C\C(O)=O
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INCHI for NP0000968 (2-Octenedioic acid)

InChI=1S/C8H12O4/c9-7(10)5-3-1-2-4-6-8(11)12/h3,5H,1-2,4,6H2,(H,9,10)(H,11,12)/b5-3+
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View in JSmol
Synonyms
ValueSource
2-OctenedioateGenerator
1-Hexene-1,6-dicarboxylateHMDB
1-Hexene-1,6-dicarboxylic acidHMDB
(2E)-Oct-2-enedioateHMDB
Chemical FormulaC8H12O4
Average Mass172.1785 Da
Monoisotopic Mass172.07356 Da
IUPAC Name(2E)-oct-2-enedioic acid
Traditional Name(E)-oct-2-enedioic acid
CAS Registry Number5698-50-0
SMILES
OC(=O)CCCC\C=C\C(O)=O
InChI Identifier
InChI=1S/C8H12O4/c9-7(10)5-3-1-2-4-6-8(11)12/h3,5H,1-2,4,6H2,(H,9,10)(H,11,12)/b5-3+
InChI KeyBNTPVRGYUHJFHN-HWKANZROSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Species Where Detected
Species NameSourceReference
Pseudomonas putidaKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Unsaturated fatty acid
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility2.06 g/LALOGPS
logP1.14ALOGPS
logP1.38ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)4.15ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity43.03 m³·mol⁻¹ChemAxon
Polarizability17.61 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000341
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021965
KNApSAcK IDC00007508
Chemspider ID4800646
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5330
PubChem Compound6079438
PDB IDNot Available
ChEBI ID89192
Good Scents IDNot Available
References
General References
  1. Pitt JJ: Gas chromatographic-mass spectrometric characterisation of unsaturated dicarboxylic acids in urine. J Chromatogr. 1990 Dec 14;534:182-9. [PubMed:2094705 ]
  2. Jin SJ, Tserng KY: Identification of isomeric unsaturated medium-chain dicarboxylic acids in human urine. J Lipid Res. 1989 Oct;30(10):1611-9. [PubMed:2614263 ]
  3. Xi X, Kwok LY, Wang Y, Ma C, Mi Z, Zhang H: Ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry MS(E)-based untargeted milk metabolomics in dairy cows with subclinical or clinical mastitis. J Dairy Sci. 2017 Jun;100(6):4884-4896. doi: 10.3168/jds.2016-11939. Epub 2017 Mar 23. [PubMed:28342601 ]
  4. Authors unspecified: Cancer Therapy Interactions With Foods and Dietary Supplements (PDQ(R)): Patient Version. 2002. [PubMed:34403226 ]
  5. Authors unspecified: Thyroid Cancer Screening (PDQ(R)): Health Professional Version. 2002. [PubMed:28876831 ]
  6. Zeng W, Huang KE, Luo Y, Li DX, Chen W, Yu XQ, Ke XH: Nontargeted urine metabolomics analysis of the protective and therapeutic effects of Citri Reticulatae Chachiensis Pericarpium on high-fat feed-induced hyperlipidemia in rats. Biomed Chromatogr. 2020 Apr;34(4):e4795. doi: 10.1002/bmc.4795. Epub 2020 Feb 12. [PubMed:31967660 ]
  7. Fan Y, Zhou X, Xia TS, Chen Z, Li J, Liu Q, Alolga RN, Chen Y, Lai MD, Li P, Zhu W, Qi LW: Human plasma metabolomics for identifying differential metabolites and predicting molecular subtypes of breast cancer. Oncotarget. 2016 Mar 1;7(9):9925-38. doi: 10.18632/oncotarget.7155. [PubMed:26848530 ]